rs343062

Variant names:

• chr7-35509456-C-T
• rs343062
• ENST00000441150.1:n.30+778G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441150.1(ENSG00000235464):​n.30+778G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,760 control chromosomes in the GnomAD database, including 9,174 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (9174 hom., cov: 31)
• Consequence: ENSG00000235464 ENST00000441150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

Genes affected

ENSG00000235464 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235464	ENST00000441150.1	n.30+778G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49253 AN: 151642 Hom.: 9163 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.336

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.325 AC: 49286 AN: 151760 Hom.: 9174 Cov.: 31 AF XY: 0.326 AC XY: 24180 AN XY: 74112

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.338

Alfa AF: 0.350 Hom.: 1236

Bravo AF: 0.319

Asia WGS AF: 0.443 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs343062; hg19: chr7-35549066;